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Karvelis E, Swanson C, Tidor B. Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity. ACS Catal 2024; 14:10491-10509. [PMID: 39050899 PMCID: PMC11264209 DOI: 10.1021/acscatal.4c01446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/16/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
The task of adapting enzymes for specific applications is often hampered by our incomplete ability to tune and tailor catalytic functions, particularly when seeking increased activity. Here, we develop and demonstrate a rational approach to address this challenge, applied to ketol-acid reductoisomerase (KARI), which has uses in industrial-scale isobutanol production. While traditional structure-based computational enzyme redesign strategies typically focus on the enzyme-bound ground state (GS) and transition state (TS), we postulated that additionally treating the underlying dynamics of complete turnover events that connect and pass through both states could further elucidate the structural properties affecting catalysis and help identify mutations that lead to increased catalytic activity. To examine the dynamics of substrate conversion with atomistic detail, we adapted and applied computational methods based on path sampling techniques to gather thousands of QM/MM simulations of attempted substrate turnover events by KARI: both productive (reactive) and unproductive (nonreactive) attempts. From these data, machine learning models were constructed and used to identify specific conformational features (interatomic distances, angles, and torsions) associated with successful, productive catalysis. Multistate protein redesign techniques were then used to select mutations that stabilized reactive-like structures over nonreactive-like ones while also meeting additional criteria consistent with enhanced specific activity. This procedure resulted in eight high-confidence enzyme mutants with a significant improvement in calculated specific activity relative to wild type (WT), with the fastest variant's increase in calculated k cat being (2 ± 1) × 104-fold. Collectively, these results suggest that introducing mutations designed to increase the population of reaction-promoting conformations of the enzyme-substrate complex before it reaches the barrier can provide an effective approach to engineering improved enzyme catalysts.
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Affiliation(s)
- Elijah Karvelis
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chloe Swanson
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Solano YJ, Kiser PD. Double-duty isomerases: a case study of isomerization-coupled enzymatic catalysis. Trends Biochem Sci 2024:S0968-0004(24)00107-5. [PMID: 38760195 DOI: 10.1016/j.tibs.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Enzymes can usually be unambiguously assigned to one of seven classes specifying the basic chemistry of their catalyzed reactions. Less frequently, two or more reaction classes are catalyzed by a single enzyme within one active site. Two examples are an isomerohydrolase and an isomero-oxygenase that catalyze isomerization-coupled reactions crucial for production of vision-supporting 11-cis-retinoids. In these enzymes, isomerization is obligately paired and mechanistically intertwined with a second reaction class. A handful of other enzymes carrying out similarly coupled isomerization reactions have been described, some of which have been subjected to detailed structure-function analyses. Herein we review these rarefied enzymes, focusing on the mechanistic and structural basis of their reaction coupling with the goal of revealing catalytic commonalities.
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Affiliation(s)
- Yasmeen J Solano
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA 92697, USA
| | - Philip D Kiser
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA 92697, USA; Department of Clinical Pharmacy Practice, University of Irvine School of Pharmacy and Pharmaceutical Sciences, Irvine, CA 92697, USA; Department of Ophthalmology, Gavin Herbert Eye Institute - Center for Translational Vision Research, University of California Irvine School of Medicine, Irvine, CA 92697, USA; Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, USA.
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3
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Characterizing the Mechanisms of Metalaxyl, Bronopol and Copper Sulfate against Saprolegnia parasitica Using Modern Transcriptomics. Genes (Basel) 2022; 13:genes13091524. [PMID: 36140692 PMCID: PMC9498376 DOI: 10.3390/genes13091524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Saprolegniasis, which is caused by Saprolegnia parasitica, leads to considerable economic losses. Recently, we showed that metalaxyl, bronopol and copper sulfate are good antimicrobial agents for aquaculture. In the current study, the efficacies of metalaxyl, bronopol and copper sulfate are evaluated by in vitro antimicrobial experiments, and the mechanism of action of these three antimicrobials on S. parasitica is explored using transcriptome technology. Finally, the potential target genes of antimicrobials on S. parasitica are identified by protein–protein interaction network analysis. Copper sulfate had the best inhibitory effect on S. parasitica, followed by bronopol. A total of 1771, 723 and 2118 DEGs upregulated and 1416, 319 and 2161 DEGs downregulated S. parasitica after three drug treatments (metalaxyl, bronopol and copper sulfate), separately. Additionally, KEGG pathway analysis also determined that there were 17, 19 and 13 significantly enriched metabolic pathways. PPI network analysis screened out three important proteins, and their corresponding genes were SPRG_08456, SPRG_03679 and SPRG_10775. Our results indicate that three antimicrobials inhibit S. parasitica growth by affecting multiple biological functions, including protein synthesis, oxidative stress, lipid metabolism and energy metabolism. Additionally, the screened key genes can be used as potential target genes of chemical antimicrobial drugs for S. parasitica.
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4
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Shah S, Lonhienne T, Murray CE, Chen Y, Dougan KE, Low YS, Williams CM, Schenk G, Walter GH, Guddat LW, Chan CX. Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development. FRONTIERS IN PLANT SCIENCE 2022; 13:909073. [PMID: 35845697 PMCID: PMC9277346 DOI: 10.3389/fpls.2022.909073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Herbicides are commonly deployed as the front-line treatment to control infestations of weeds in native ecosystems and among crop plants in agriculture. However, the prevalence of herbicide resistance in many species is a major global challenge. The specificity and effectiveness of herbicides acting on diverse weed species are tightly linked to targeted proteins. The conservation and variance at these sites among different weed species remain largely unexplored. Using novel genome data in a genome-guided approach, 12 common herbicide-target genes and their coded proteins were identified from seven species of Weeds of National Significance in Australia: Alternanthera philoxeroides (alligator weed), Lycium ferocissimum (African boxthorn), Senecio madagascariensis (fireweed), Lantana camara (lantana), Parthenium hysterophorus (parthenium), Cryptostegia grandiflora (rubber vine), and Eichhornia crassipes (water hyacinth). Gene and protein sequences targeted by the acetolactate synthase (ALS) inhibitors and glyphosate were recovered. Compared to structurally resolved homologous proteins as reference, high sequence conservation was observed at the herbicide-target sites in the ALS (target for ALS inhibitors), and in 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (target for glyphosate). Although the sequences are largely conserved in the seven phylogenetically diverse species, mutations observed in the ALS proteins of fireweed and parthenium suggest resistance of these weeds to ALS-inhibiting and other herbicides. These protein sites remain as attractive targets for the development of novel inhibitors and herbicides. This notion is reinforced by the results from the phylogenetic analysis of the 12 proteins, which reveal a largely consistent vertical inheritance in their evolutionary histories. These results demonstrate the utility of high-throughput genome sequencing to rapidly identify and characterize gene targets by computational methods, bypassing the experimental characterization of individual genes. Data generated from this study provide a useful reference for future investigations in herbicide discovery and development.
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Affiliation(s)
- Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Cody-Ellen Murray
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine E. Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yu Shang Low
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Gimme H. Walter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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5
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Lemaire ON, Müller MC, Kahnt J, Wagner T. Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen. Biomolecules 2021; 11:1679. [PMID: 34827677 PMCID: PMC8615647 DOI: 10.3390/biom11111679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg2+-site, the Mg2+-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs.
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Affiliation(s)
- Olivier Nicolas Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; (O.N.L.); (M.-C.M.)
| | - Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; (O.N.L.); (M.-C.M.)
| | - Jörg Kahnt
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany;
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; (O.N.L.); (M.-C.M.)
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6
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Zhuang YC, Ye DS, Weng SU, Tsai HHG. Double Proton Transfer during a Novel Tertiary α-Ketol Rearrangement in Ketol-Acid Reductoisomerase: A Water-Mediated, Metal-Catalyzed, Base-Induced Mechanism. J Phys Chem B 2021; 125:11893-11906. [PMID: 34618450 DOI: 10.1021/acs.jpcb.1c07137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(KARI) catalyzes the conversion of (S)-2-acetolactate or (S)-2-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-alkylbutyrate, the second step in the biosynthesis of branched chain amino acids (BCAAs). Because the BCAA biosynthetic pathway is present in bacteria, plants, and fungi, but absent in animals, it is an excellent target for the development of new-generation antibiotics and herbicides. Nevertheless, the mechanism of the KARI-catalyzed reaction has not yet been fully solved. In this study, we used iterative molecular dynamics (MD) flexible fitting-Rosetta techniques to optimize the three-dimensional solution structure of archaea KARI from Sulfolobus solfataricus (Sso-KARI) determined from cryo-electron microscopy. On the basis of the structure of the Sso-KARI/2Mg2+/NADH/(S)-2-acetolactate complex, we deciphered the catalytic mechanism of the KARI-mediated reaction through hybrid quantum mechanics/molecular mechanics MD simulations in conjunction with umbrella sampling. With an activation energy of only 6.06 kcal/mol, a water-mediated, metal-catalyzed, base-induced (WMMCBI) mechanism was preferred for deprotonation of the tertiary OH group of (S)-2-acetolactate in Sso-KARI. The WMMCBI mechanism for double proton transfer occurred within a proton wire route with two steps involving the formation of hydroxide: (i) Glu233 served as a general base to deprotonate the Mg2+-bound water, forming a hydroxide-coordinated Mg2+ ion; (ii) this hydroxide ion acted as a strong base that rapidly deprotonated the ternary OH group of the substrate. In contrast, the direct deprotonation of the substrate by Glu233 was kinetically unfavorable. This mechanism suggests a novel approach for designing catalysts for deprotonation and provides clues for the development of new-generation antibiotics and herbicides.
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Affiliation(s)
- Yi-Chuan Zhuang
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
| | - Dong-Sheng Ye
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
| | - Sheng-Uei Weng
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
| | - Hui-Hsu Gavin Tsai
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan.,Research Center of New-Generation Light-Driven Photovoltaic Modules, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
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7
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Liang YF, Long ZX, Zhang YJ, Luo CY, Yan LT, Gao WY, Li H. The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications. Biochimie 2021; 184:72-87. [PMID: 33607240 DOI: 10.1016/j.biochi.2021.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/27/2022]
Abstract
l-Valine, l-isoleucine, and l-leucine are three key proteinogenic amino acids, and they are also the essential amino acids required for mammalian growth, possessing important and to some extent, special physiological and biological functions. Because of the branched structures in their carbon chains, they are also named as branched-chain amino acids (BCAAs). This review will highlight the advance in studies of the enzymes involved in the biosynthetic pathway of BCAAs, concentrating on their chemical mechanisms and applications in screening herbicides and antibacterial agents. The uses of some of these enzymes in lab scale organic synthesis are also discussed.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Zi-Xian Long
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Ya-Jian Zhang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Cai-Yun Luo
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Le-Tian Yan
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
| | - Heng Li
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
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8
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Lin X, Kurz JL, Patel KM, Wun SJ, Hussein WM, Lonhienne T, West NP, McGeary RP, Schenk G, Guddat LW. Discovery of a Pyrimidinedione Derivative with Potent Inhibitory Activity against Mycobacterium tuberculosis Ketol-Acid Reductoisomerase. Chemistry 2021; 27:3130-3141. [PMID: 33215746 DOI: 10.1002/chem.202004665] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 12/26/2022]
Abstract
New drugs aimed at novel targets are urgently needed to combat the increasing rate of drug-resistant tuberculosis (TB). Herein, the National Cancer Institute Developmental Therapeutic Program (NCI-DTP) chemical library was screened against a promising new target, ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid (BCAA) biosynthesis pathway. From this library, 6-hydroxy-2-methylthiazolo[4,5-d]pyrimidine-5,7(4H,6H)-dione (NSC116565) was identified as a potent time-dependent inhibitor of Mycobacterium tuberculosis (Mt) KARI with a Ki of 95.4 nm. Isothermal titration calorimetry studies showed that this inhibitor bound to MtKARI in the presence and absence of the cofactor, nicotinamide adenine dinucleotide phosphate (NADPH), which was confirmed by crystal structures of the compound in complex with closely related Staphylococcus aureus KARI. It is also shown that NSC116565 inhibits the growth of H37Ra and H37Rv strains of Mt with MIC50 values of 2.93 and 6.06 μm, respectively. These results further validate KARI as a TB drug target and show that NSC116565 is a promising lead for anti-TB drug development.
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Affiliation(s)
- Xin Lin
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Julia L Kurz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Khushboo M Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Shun Jie Wun
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia.,Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan University, Helwan, Egypt
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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9
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Wun SJ, Johnson LA, You L, McGeary RP, Brueck T, Schenk G, Guddat LW. Inhibition studies of ketol-acid reductoisomerases from pathogenic microorganisms. Arch Biochem Biophys 2020; 692:108516. [DOI: 10.1016/j.abb.2020.108516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 10/23/2022]
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10
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Bayaraa T, Kurz JL, Patel KM, Hussein WM, Bilyj JK, West NP, Schenk G, McGeary RP, Guddat LW. Discovery, Synthesis and Evaluation of a Ketol-Acid Reductoisomerase Inhibitor. Chemistry 2020; 26:8958-8968. [PMID: 32198779 DOI: 10.1002/chem.202000899] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/13/2020] [Indexed: 11/10/2022]
Abstract
Ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway, is a potential drug target for bacterial infections including Mycobacterium tuberculosis. Here, we have screened the Medicines for Malaria Venture Pathogen Box against purified M. tuberculosis (Mt) KARI and identified two compounds that have Ki values below 200 nm. In Mt cell susceptibility assays one of these compounds exhibited an IC50 value of 0.8 μm. Co-crystallization of this compound, 3-((methylsulfonyl)methyl)-2H-benzo[b][1,4]oxazin-2-one (MMV553002), in complex with Staphylococcus aureus KARI, which has 56 % identity with Mt KARI, NADPH and Mg2+ yielded a structure to 1.72 Å resolution. However, only a hydrolyzed product of the inhibitor (i.e. 3-(methylsulfonyl)-2-oxopropanic acid, missing the 2-aminophenol attachment) is observed in the active site. Surprisingly, Mt cell susceptibility assays showed that the 2-aminophenol product is largely responsible for the anti-TB activity of the parent compound. Thus, 3-(methylsulfonyl)-2-oxopropanic acid was identified as a potent KARI inhibitor that could be further explored as a potential biocidal agent and we have shown 2-aminophenol, as an anti-TB drug lead, especially given it has low toxicity against human cells. The study highlights that careful analysis of broad screening assays is required to correctly interpret cell-based activity data.
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Affiliation(s)
- Tenuun Bayaraa
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Julia L Kurz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Khushboo M Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia.,Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan University, Helwan, Egypt
| | - Jessica K Bilyj
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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11
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Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae. CRYSTALS 2019. [DOI: 10.3390/cryst9110551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biosynthesis of branched-chain amino acids (BCAAs), including isoleucine, leucine and valine, is required for survival and virulence of a bacterial pathogen such as Streptococcus pneumoniae. IlvC, a ketol-acid reductoisomerase (E.C. 1.1.1.86) with NADP(H) and Mg2+ as cofactors from the pathogenic Streptococcus pneumoniae (SpIlvC), catalyzes the second step in the BCAA biosynthetic pathway. To elucidate the structural basis for the IlvC-mediated reaction, we determined the crystal structure of SpIlvC at 1.69 Å resolution. The crystal structure of SpIlvC contains an asymmetric dimer in which one subunit is in apo-form and the other in NADP(H) and Mg2+-bound form. Crystallographic analysis combined with an activity assay and small-angle X-ray scattering suggested that SpIlvC retains dimeric arrangement in solution and that D83 in the NADP(H) binding site and E195 in the Mg2+ binding site are the most critical in the catalytic activity of SpIlvC. Crystal structures of SpIlvC mutants (R49E, D83G, D191G and E195S) revealed local conformational changes only in the NADP(H) binding site. Taken together, our results establish the molecular mechanism for understanding functions of SpIlvC in pneumococcal growth and virulence.
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12
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Joyard J, Lichtenthaler HK. Tribute Roland Douce, 1939-2018. PHOTOSYNTHESIS RESEARCH 2019; 141:131-142. [PMID: 30877517 DOI: 10.1007/s11120-019-00634-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
On November 4, 2018, Roland Douce, Professor Emeritus at the University of Grenoble, France, died at the age of 79. In Grenoble, where he spent most of his scientific career, Roland Douce created a world-renowned school of plant science, studying the structure, functions, and interactions of plant organelles involved in photosynthesis, respiration, and photorespiration. His main achievements concern the chemical and functional characterization of chloroplast envelope membranes, the demonstration of the uniqueness of plant mitochondria, and the integration of metabolism within the plant cell, among manifold activities. Roland Douce devoted his whole life to science and research with passion and enthusiasm: he was a true charismatic leader.
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Affiliation(s)
- Jacques Joyard
- Laboratoire de Physiologie cellulaire et végétale, Institut de Recherche Interdisciplinaire de Grenoble, Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France.
| | - Hartmut K Lichtenthaler
- Botany 2 (Molecular Biology and Biochemistry of Plants), Karlsruhe Institute of Technology, Kaiserstr. 12, 76133, Karlsruhe, Germany
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13
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Chen CY, Chang YC, Lin BL, Lin KF, Huang CH, Hsieh DL, Ko TP, Tsai MD. Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase. J Am Chem Soc 2019; 141:6136-6140. [DOI: 10.1021/jacs.9b01354] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Chin-Yu Chen
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | | | | | - Kuan-Fu Lin
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chun-Hsiang Huang
- Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Dong-Lin Hsieh
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | | | - Ming-Daw Tsai
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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14
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Bonk B, Weis JW, Tidor B. Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis. J Am Chem Soc 2019; 141:4108-4118. [PMID: 30761897 PMCID: PMC6407039 DOI: 10.1021/jacs.8b13879] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Indexed: 11/28/2022]
Abstract
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. Here, we investigate the structural and dynamic drivers of enzyme catalysis for the rate-limiting step of the industrially important enzyme ketol-acid reductoisomerase (KARI) and identify a region of the conformational space of the bound enzyme-substrate complex that, when populated, leads to large increases in reactivity. We apply computational statistical mechanical methods that implement transition interface sampling to simulate the kinetics of the reaction and combine this with machine learning techniques from artificial intelligence to select features relevant to reactivity and to build predictive models for reactive trajectories. We find that conformational descriptors alone, without the need for dynamic ones, are sufficient to predict reactivity with greater than 85% accuracy (90% AUC). Key descriptors distinguishing reactive from almost-reactive trajectories quantify substrate conformation, substrate bond polarization, and metal coordination geometry and suggest their role in promoting substrate reactivity. Moreover, trajectories constrained to visit a region of the reactant well, separated from the rest by a simple hyperplane defined by ten conformational parameters, show increases in computed reactivity by many orders of magnitude. This study provides evidence for the existence of reactivity promoting regions within the conformational space of the enzyme-substrate complex and develops methodology for identifying and validating these particularly reactive regions of phase space. We suggest that identification of reactivity promoting regions and re-engineering enzymes to preferentially populate them may lead to significant rate enhancements.
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Affiliation(s)
- Brian
M. Bonk
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - James W. Weis
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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15
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He FQ, Liu XH, Wang BL, Li ZM. Synthesis and biological activity of new 1-[4-(substituted)-piperazin-1-ylmethyl]-1H-benzotriazole. JOURNAL OF CHEMICAL RESEARCH 2019. [DOI: 10.3184/030823406780199703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A new kind of benzotriazole derivatives has been designed and synthesised. The structures of all of the title compounds were characterised by 1H NMR, IR, MS and elemental analyses. Herbicidal activities of the benzotrizole derivatives were evaluated with barnyard grass and rape cup and KARI tests. The results showed that compounds exhibited weak herbicidal activities against barnyardgrass and rape and KARI enzyme.
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Affiliation(s)
- Feng-qi He
- The Research Institute Elemento-Organic Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Xing-hai Liu
- The Research Institute Elemento-Organic Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Bao-lei Wang
- The Research Institute Elemento-Organic Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Zheng-Ming Li
- The Research Institute Elemento-Organic Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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16
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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17
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NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius. Sci Rep 2018; 8:7176. [PMID: 29739976 PMCID: PMC5940873 DOI: 10.1038/s41598-018-25361-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/19/2018] [Indexed: 11/13/2022] Open
Abstract
Ketol-acid reductoisomerase (KARI) is a bifunctional enzyme in the second step of branched-chain amino acids biosynthetic pathway. Most KARIs prefer NADPH as a cofactor. However, KARI with a preference for NADH is desirable in industrial applications including anaerobic fermentation for the production of branched-chain amino acids or biofuels. Here, we characterize a thermoacidophilic archaeal Sac-KARI from Sulfolobus acidocaldarius and present its crystal structure at a 1.75-Å resolution. By comparison with other holo-KARI structures, one sulphate ion is observed in each binding site for the 2′-phosphate of NADPH, implicating its NADPH preference. Sac-KARI has very high affinity for NADPH and NADH, with KM values of 0.4 μM for NADPH and 6.0 μM for NADH, suggesting that both are good cofactors at low concentrations although NADPH is favoured over NADH. Furthermore, Sac-KARI can catalyze 2(S)-acetolactate (2S-AL) with either cofactor from 25 to 60 °C, but the enzyme has higher activity by using NADPH. In addition, the catalytic activity of Sac-KARI increases significantly with elevated temperatures and reaches an optimum at 60 °C. Bi-cofactor utilization and the thermoactivity of Sac-KARI make it a potential candidate for use in metabolic engineering or industrial applications under anaerobic or harsh conditions.
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18
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Han D, Qi X, Myhrvold C, Wang B, Dai M, Jiang S, Bates M, Liu Y, An B, Zhang F, Yan H, Yin P. Single-stranded DNA and RNA origami. Science 2017; 358:eaao2648. [PMID: 29242318 PMCID: PMC6384012 DOI: 10.1126/science.aao2648] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022]
Abstract
Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology.
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Affiliation(s)
- Dongran Han
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Xiaodong Qi
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Cameron Myhrvold
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Bei Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Mingjie Dai
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Shuoxing Jiang
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Maxwell Bates
- BioNano Research Group, Autodesk Life Sciences, Pier 9, San Francisco, CA 94111, USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Byoungkwon An
- BioNano Research Group, Autodesk Life Sciences, Pier 9, San Francisco, CA 94111, USA.
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Peng Yin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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19
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Patel KM, Teran D, Zheng S, Kandale A, Garcia M, Lv Y, Schembri MA, McGeary RP, Schenk G, Guddat LW. Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity. Chemistry 2017; 23:18289-18295. [PMID: 28975665 DOI: 10.1002/chem.201704481] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Indexed: 01/19/2023]
Abstract
Ketol-acid reductoisomerase (KARI) is an NAD(P)H and Mg2+ -dependent enzyme of the branched-chain amino acid (BCAA) biosynthesis pathway. Here, the first crystal structures of Staphylococcus aureus (Sa) KARI in complex with two transition state analogues, cyclopropane-1,1-dicarboxylate (CPD) and N-isopropyloxalyl hydroxamate (IpOHA) are reported. These compounds bind competitively and in multi-dentate manner to KARI with Ki values of 2.73 μm and 7.9 nm, respectively; however, IpOHA binds slowly to the enzyme. Interestingly, intact IpOHA is present in only ≈25 % of binding sites, whereas its deoxygenated form is present in the remaining sites. This deoxy form of IpOHA binds rapidly to Sa KARI, but with much weaker affinity (Ki =21 μm). Thus, our data pinpoint the origin of the slow binding mechanism of IpOHA. Furthermore, we propose that CPD mimics the early stage of the catalytic reaction (preceding the reduction step), whereas IpOHA mimics the late stage (after the reduction took place). These structural insights will guide strategies to design potent and rapidly binding derivatives of these compounds for the development of novel biocides.
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Affiliation(s)
- Khushboo M Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - David Teran
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Shan Zheng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ajit Kandale
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Mario Garcia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - You Lv
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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20
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Tadrowski S, Pedroso MM, Sieber V, Larrabee JA, Guddat LW, Schenk G. Metal Ions Play an Essential Catalytic Role in the Mechanism of Ketol-Acid Reductoisomerase. Chemistry 2016; 22:7427-36. [PMID: 27136273 DOI: 10.1002/chem.201600620] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Indexed: 01/13/2023]
Abstract
Ketol-acid reductoisomerase (KARI) is a Mg(2+) -dependent enzyme in the branched-chain amino acid biosynthesis pathway. It catalyses a complex two-part reaction: an alkyl migration followed by a NADPH-dependent reduction. Both reactions occur within the one active site, but in particular, the mechanism of the isomerisation step is poorly understood. Here, using a combination of kinetic, thermodynamic and spectroscopic techniques, the reaction mechanisms of both Escherichia coli and rice KARI have been investigated. We propose a conserved mechanism of catalysis, whereby a hydroxide, bridging the two Mg(2+) ions in the active site, initiates the reaction by abstracting a proton from the C2 alcohol group of the substrate. While the μ-hydroxide-bridged dimetallic centre is pre-assembled in the bacterial enzyme, in plant KARI substrate binding leads to a reduction of the metal-metal distance with the concomitant formation of a hydroxide bridge. Only Mg(2+) is capable of promoting the isomerisation reaction, likely to be due to non-competent substrate binding in the presence of other metal ions.
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Affiliation(s)
- Sonya Tadrowski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Volker Sieber
- Straubing Center of Science, Technische Universität München, Straubing, Germany
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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21
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Galili G, Amir R, Fernie AR. The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:153-78. [PMID: 26735064 DOI: 10.1146/annurev-arplant-043015-112213] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.
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Affiliation(s)
- Gad Galili
- Department of Plant Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Rachel Amir
- Laboratory of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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22
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Biodegradation of zearalenone by Saccharomyces cerevisiae: Possible involvement of ZEN responsive proteins of the yeast. J Proteomics 2016; 143:416-423. [PMID: 27109348 DOI: 10.1016/j.jprot.2016.04.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 01/06/2023]
Abstract
UNLABELLED The mycotoxin zearalenone, also known as F-2 mycotoxin or RAL is a potent estrogenic metabolite produced by some Gibberella and Fusarium species. It is a common contaminant of cereal crops, livestock and poultry products. However, detoxification of zearalenone (ZEN) remains a challenge. Recently, biological approach for ZEN detoxification is being explored. In this study, we investigated the biodegradation of ZEN by using Saccharomyces cerevisiae and the possible mechanisms involved. The findings revealed that, after 48h of incubation of S. cerevisiae in combination with ZEN, the ZEN was completely degraded by S. cerevisiae. On the contrary, heat-killed cells and cell-free culture filtrates of S. cerevisiae could not degrade ZEN. Furthermore, addition of cycloheximide to S. cerevisiae combined with ZEN at time 0h prevented ZEN degradation, while addition of cycloheximide at 12h significantly slowed down degradation. The results also indicated cellular proteomics of S. cerevisiae. Several differential proteins were identified, most of which were related to basic metabolism. BIOLOGICAL SIGNIFICANCE The findings revealed that, after 48h of incubating ZEN together with S. cerevisiae, ZEN was completely degraded by S. cerevisiae. The mechanisms involved in the degradation of ZEN by S. cerevisiae may be the production of associated intracellular and extracellular enzymes, which have the ability to degrade ZEN. In addition, there were some functional proteins produced by S. cerevisiae, indicating that the basic metabolism of S. cerevisiae was improved when ZEN was added. This novel discovery by the authors, will greatly contribute to the field of biodegradation of mycotoxin by antagonists. The authors also believed this innovation will open the grounds for further research and improvement of S. cerevisiae in the field of biodegradation.
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23
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Lv Y, Kandale A, Wun SJ, McGeary RP, Williams SJ, Kobe B, Sieber V, Schembri MA, Schenk G, Guddat LW. Crystal structure of
Mycobacterium tuberculosis
ketol‐acid reductoisomerase at 1.0 Å resolution – a potential target for anti‐tuberculosis drug discovery. FEBS J 2016; 283:1184-96. [DOI: 10.1111/febs.13672] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/18/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Affiliation(s)
- You Lv
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Ajit Kandale
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Shun Jie Wun
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
- Institute for Molecular Bioscience University of Queensland Brisbane Australia
| | - Volker Sieber
- Straubing Center of Science Technische Universität München Straubing Germany
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
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24
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Cahn JKB, Brinkmann-Chen S, Buller AR, Arnold FH. Artificial domain duplication replicates evolutionary history of ketol-acid reductoisomerases. Protein Sci 2015; 25:1241-8. [PMID: 26644020 DOI: 10.1002/pro.2852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/01/2015] [Indexed: 11/11/2022]
Abstract
The duplication of protein structural domains has been proposed as a common mechanism for the generation of new protein folds. A particularly interesting case is the class II ketol-acid reductoisomerase (KARI), which putatively arose from an ancestral class I KARI by duplication of the C-terminal domain and corresponding loss of obligate dimerization. As a result, the class II enzymes acquired a deeply embedded figure-of-eight knot. To test this evolutionary hypothesis we constructed a novel class II KARI by duplicating the C-terminal domain of a hyperthermostable class I KARI. The new protein is monomeric, as confirmed by gel filtration and X-ray crystallography, and has the deeply knotted class II KARI fold. Surprisingly, its catalytic activity is nearly unchanged from the parent KARI. This provides strong evidence in support of domain duplication as the mechanism for the evolution of the class II KARI fold and demonstrates the ability of domain duplication to generate topological novelty in a function-neutral manner.
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Affiliation(s)
- Jackson K B Cahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Andrew R Buller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
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25
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Lim NCH, Jackson SE. Molecular knots in biology and chemistry. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354101. [PMID: 26291690 DOI: 10.1088/0953-8984/27/35/354101] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.
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Affiliation(s)
- Nicole C H Lim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. Faculty of Sciences, Universiti Brunei Darussalam, Gadong BE 1410, Brunei Darussalam
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26
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Wong WC, Yap CK, Eisenhaber B, Eisenhaber F. dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity. Biol Direct 2015; 10:39. [PMID: 26228544 PMCID: PMC4521371 DOI: 10.1186/s13062-015-0068-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/20/2015] [Indexed: 11/10/2022] Open
Abstract
Background Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies. The latter is either due to positional sequence conservation as a result of a very simple, physically induced pattern or integral sequence properties that are critical for function. Furthermore, against the backdrop that the number of well-studied proteins continues to grow at a slow rate, it necessitates for a search methodology to dive deeper into the sequence similarity space to connect the unknown sequences to the well-studied ones, albeit more distant, for biological function postulations. Results Based on our previous work of dissecting the hidden markov model (HMMER) based similarity score into fold-critical and the non-globular contributions to improve homology inference, we propose a framework-dissectHMMER, that identifies more fold-related domain hits from standard HMMER searches. Subsequent statistical stratification of the fold-related hits into cohorts of functionally-related domains allows for the function postulation of the query sequence. Briefly, the technical problems as to how to recognize non-globular parts in the domain model, resolve contradictory HMMER2/HMMER3 results and evaluate fold-related domain hits for homology, are addressed in this work. The framework is benchmarked against a set of SCOP-to-Pfam domain models. Despite being a sequence-to-profile method, dissectHMMER performs favorably against a profile-to-profile based method-HHsuite/HHsearch. Examples of function annotation using dissectHMMER, including the function discovery of an uncharacterized membrane protein Q9K8K1_BACHD (WP_010899149.1) as a lactose/H+ symporter, are presented. Finally, dissectHMMER webserver is made publicly available at http://dissecthmmer.bii.a-star.edu.sg. Conclusions The proposed framework-dissectHMMER, is faithful to the original inception of the sequence homology concept while improving upon the existing HMMER search tool through the rescue of statistically evaluated false-negative yet fold-related domain hits to the query sequence. Overall, this translates into an opportunity for any novel protein sequence to be functionally characterized. Reviewers This article was reviewed by Masanori Arita, Shamil Sunyaev and L. Aravind. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0068-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wing-Cheong Wong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
| | - Choon-Kong Yap
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore. .,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore, 117597, Singapore. .,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
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Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases. Biochem J 2015; 468:475-84. [PMID: 25849365 DOI: 10.1042/bj20150183] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/07/2015] [Indexed: 11/17/2022]
Abstract
Although most sequenced members of the industrially important ketol-acid reductoisomerase (KARI) family are class I enzymes, structural studies to date have focused primarily on the class II KARIs, which arose through domain duplication. In the present study, we present five new crystal structures of class I KARIs. These include the first structure of a KARI with a six-residue β2αB (cofactor specificity determining) loop and an NADPH phosphate-binding geometry distinct from that of the seven- and 12-residue loops. We also present the first structures of naturally occurring KARIs that utilize NADH as cofactor. These results show insertions in the specificity loops that confounded previous attempts to classify them according to loop length. Lastly, we explore the conformational changes that occur in class I KARIs upon binding of cofactor and metal ions. The class I KARI structures indicate that the active sites close upon binding NAD(P)H, similar to what is observed in the class II KARIs of rice and spinach and different from the opening of the active site observed in the class II KARI of Escherichia coli. This conformational change involves a decrease in the bending of the helix that runs between the domains and a rearrangement of the nicotinamide-binding site.
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28
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McSkimming A, Chan B, Bhadbhade MM, Ball GE, Colbran SB. Bio-Inspired Transition Metal-Organic Hydride Conjugates for Catalysis of Transfer Hydrogenation: Experiment and Theory. Chemistry 2014; 21:2821-34. [DOI: 10.1002/chem.201405129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Indexed: 11/07/2022]
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29
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Verdel-Aranda K, López-Cortina ST, Hodgson DA, Barona-Gómez F. Molecular annotation of ketol-acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity. Microb Biotechnol 2014; 8:239-52. [PMID: 25296650 PMCID: PMC4353338 DOI: 10.1111/1751-7915.12175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022] Open
Abstract
The 6-phosphogluconate dehydrogenase superfamily oxidize and reduce a wide range of substrates, making their functional annotation challenging. Ketol-acid reductoisomerase (KARI), encoded by the ilvC gene in branched-chain amino acids biosynthesis, is a promiscuous reductase enzyme within this superfamily. Here, we obtain steady-state enzyme kinetic parameters for 10 IlvC homologues from the genera Streptomyces and Corynebacterium, upon eight selected chemically diverse substrates, including some not normally recognized by enzymes of this superfamily. This biochemical data suggested a Streptomyces biosynthetic interlock between proline and the branched-chain amino acids, mediated by enzyme substrate promiscuity, which was confirmed via mutagenesis and complementation analyses of the proC, ilvC1 and ilvC2 genes in Streptomyces coelicolor. Moreover, both ilvC orthologues and paralogues were analysed, such that the relationship between gene duplication and functional diversification could be explored. The KARI paralogues present in S. coelicolor and Streptomyces lividans, despite their conserved high sequence identity (97%), were shown to be more promiscuous, suggesting a recent functional diversification. In contrast, the KARI paralogue from Streptomyces viridifaciens showed selectivity towards the synthesis of valine precursors, explaining its recruitment within the biosynthetic gene cluster of valanimycin. These results allowed us to assess substrate promiscuity indices as a tool to annotate new molecular functions with metabolic implications.
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Affiliation(s)
- Karina Verdel-Aranda
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Irapuato, Guanajuato, CP36822, México
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30
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Brinkmann-Chen S, Cahn JKB, Arnold FH. Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab Eng 2014; 26:17-22. [PMID: 25172159 DOI: 10.1016/j.ymben.2014.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/01/2014] [Accepted: 08/19/2014] [Indexed: 11/25/2022]
Abstract
All members of the ketol-acid reductoisomerase (KARI) enzyme family characterized to date have been shown to prefer the nicotinamide adenine dinucleotide phosphate hydride (NADPH) cofactor to nicotinamide adenine dinucleotide hydride (NADH). However, KARIs with the reversed cofactor preference are desirable for industrial applications, including anaerobic fermentation to produce branched-chain amino acids. By applying insights gained from structural and engineering studies of this enzyme family to a comprehensive multiple sequence alignment of KARIs, we identified putative NADH-utilizing KARIs and characterized eight whose catalytic efficiencies using NADH were equal to or greater than NADPH. These are the first naturally NADH-preferring KARIs reported and demonstrate that this property has evolved independently multiple times, using strategies unlike those used previously in the laboratory to engineer a KARI cofactor switch.
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Affiliation(s)
- S Brinkmann-Chen
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA.
| | - J K B Cahn
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA.
| | - F H Arnold
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA.
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31
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Ponnuswamy N, Cougnon FBL, Pantoş GD, Sanders JKM. Homochiral and meso Figure Eight Knots and a Solomon Link. J Am Chem Soc 2014; 136:8243-51. [DOI: 10.1021/ja4125884] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nandhini Ponnuswamy
- University
Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, U.K
| | - Fabien B. L. Cougnon
- University
Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, U.K
| | - G. Dan Pantoş
- University
Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, U.K
- Department
of Chemistry, University of Bath, BA 7AY, Bath, U.K
| | - Jeremy K. M. Sanders
- University
Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, U.K
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32
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General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH. Proc Natl Acad Sci U S A 2013; 110:10946-51. [PMID: 23776225 DOI: 10.1073/pnas.1306073110] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To date, efforts to switch the cofactor specificity of oxidoreductases from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) have been made on a case-by-case basis with varying degrees of success. Here we present a straightforward recipe for altering the cofactor specificity of a class of NADPH-dependent oxidoreductases, the ketol-acid reductoisomerases (KARIs). Combining previous results for an engineered NADH-dependent variant of Escherichia coli KARI with available KARI crystal structures and a comprehensive KARI-sequence alignment, we identified key cofactor specificity determinants and used this information to construct five KARIs with reversed cofactor preference. Additional directed evolution generated two enzymes having NADH-dependent catalytic efficiencies that are greater than the wild-type enzymes with NADPH. High-resolution structures of a wild-type/variant pair reveal the molecular basis of the cofactor switch.
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33
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Fan J, Cui Y, Huang J, Wang W, Yin W, Hu Z, Li Y. Suppression subtractive hybridization reveals transcript profiling of Chlorella under heterotrophy to photoautotrophy transition. PLoS One 2012; 7:e50414. [PMID: 23209737 PMCID: PMC3510161 DOI: 10.1371/journal.pone.0050414] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/19/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Microalgae have been extensively investigated and exploited because of their competitive nutritive bioproducts and biofuel production ability. Chlorella are green algae that can grow well heterotrophically and photoautotrophically. Previous studies proved that shifting from heterotrophy to photoautotrophy in light-induced environments causes photooxidative damage as well as distinct physiologic features that lead to dynamic changes in Chlorella intracellular components, which have great potential in algal health food and biofuel production. However, the molecular mechanisms underlying the trophic transition remain unclear. METHODOLOGY/PRINCIPAL FINDINGS In this study, suppression subtractive hybridization strategy was employed to screen and characterize genes that are differentially expressed in response to the light-induced shift from heterotrophy to photoautotrophy. Expressed sequence tags (ESTs) were obtained from 770 and 803 randomly selected clones among the forward and reverse libraries, respectively. Sequence analysis identified 544 unique genes in the two libraries. The functional annotation of the assembled unigenes demonstrated that 164 (63.1%) from the forward library and 62 (21.8%) from the reverse showed significant similarities with the sequences in the NCBI non-redundant database. The time-course expression patterns of 38 selected differentially expressed genes further confirmed their responsiveness to a diverse trophic status. The majority of the genes enriched in the subtracted libraries were associated with energy metabolism, amino acid metabolism, protein synthesis, carbohydrate metabolism, and stress defense. CONCLUSIONS/SIGNIFICANCE The data presented here offer the first insights into the molecular foundation underlying the diverse microalgal trophic niche. In addition, the results can be used as a reference for unraveling candidate genes associated with the transition of Chlorella from heterotrophy to photoautotrophy, which holds great potential for further improving its lipid and nutrient production.
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Affiliation(s)
- Jianhua Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People’s Republic of China
| | - Yanbin Cui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People’s Republic of China
| | - Jianke Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People’s Republic of China
| | - Weiliang Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People’s Republic of China
| | - Weibo Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Zanmin Hu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, People’s Republic of China
- * E-mail: (YL); (ZH)
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People’s Republic of China
- * E-mail: (YL); (ZH)
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34
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Bacterial and plant ketol-acid reductoisomerases have different mechanisms of induced fit during the catalytic cycle. J Mol Biol 2012; 424:168-79. [PMID: 23036858 DOI: 10.1016/j.jmb.2012.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 09/09/2012] [Accepted: 09/24/2012] [Indexed: 11/21/2022]
Abstract
Ketol-acid reductoisomerase (KARI) is the second enzyme in the branched-chain amino acid biosynthesis pathway, which is found in plants, fungi and bacteria but not in animals. This difference in metabolism between animals and microorganisms makes KARI an attractive target for the development of antimicrobial agents. Herein we report the crystal structure of Escherichia coli KARI in complex with Mg(2+) and NADPH at 2.3Å resolution. Ultracentrifugation studies confirm that the enzyme exists as a tetramer in solution, and isothermal titration calorimetry shows that the binding of Mg(2+) increases structural disorder while the binding of NADPH increases the structural rigidity of the enzyme. Comparison of the structure of the E. coli KARI-Mg(2+)-NADPH complex with that of enzyme in the absence of cofactors shows that the binding of Mg(2+) and NADPH opens the interface between the N- and C-domains, thereby allowing access for the substrates to bind: the existence of only a small opening between the domains in the crystal structure of the unliganded enzyme signifies restricted access to the active site. This observation contrasts with that in the plant enzyme, where the N-domain can rotate freely with respect to the C-domain until the binding of Mg(2+) and/or NADPH stabilizes the relative positions of these domains. Support is thereby provided for the idea that plant and bacterial KARIs have evolved different mechanisms of induced fit to prepare the active site for catalysis.
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35
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Kumari S, van der Hoorn RAL. A structural biology perspective on bioactive small molecules and their plant targets. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:480-8. [PMID: 21803639 DOI: 10.1016/j.pbi.2011.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/01/2011] [Accepted: 06/14/2011] [Indexed: 05/08/2023]
Abstract
Structural biology efforts in recent years have generated numerous co-crystal structures of bioactive small molecules interacting with their plant targets. These studies include the targets of various phytohormones, pathogen-derived effectors, herbicides and other bioactive compounds. Here we discuss that this collection of structures contains excellent examples of nine collective observations: molecular glues, allostery, inhibitors, molecular mimicry, promiscuous binding sites, unexpected electron densities, natural selection at atomic resolution, and applications in structure-guided mutagenesis and small molecule design.
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Affiliation(s)
- Selva Kumari
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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36
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Bastian S, Liu X, Meyerowitz JT, Snow CD, Chen MMY, Arnold FH. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab Eng 2011; 13:345-52. [PMID: 21515217 DOI: 10.1016/j.ymben.2011.02.004] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/04/2011] [Accepted: 02/10/2011] [Indexed: 11/19/2022]
Abstract
2-methylpropan-1-ol (isobutanol) is a leading candidate biofuel for the replacement or supplementation of current fossil fuels. Recent work has demonstrated glucose to isobutanol conversion through a modified amino acid pathway in a recombinant organism. Although anaerobic conditions are required for an economically competitive process, only aerobic isobutanol production has been feasible due to an imbalance in cofactor utilization. Two of the pathway enzymes, ketol-acid reductoisomerase and alcohol dehydrogenase, require nicotinamide dinucleotide phosphate (NADPH); glycolysis, however, produces only nicotinamide dinucleotide (NADH). Here, we compare two solutions to this imbalance problem: (1) over-expression of pyridine nucleotide transhydrogenase PntAB and (2) construction of an NADH-dependent pathway, using engineered enzymes. We demonstrate that an NADH-dependent pathway enables anaerobic isobutanol production at 100% theoretical yield and at higher titer and productivity than both the NADPH-dependent pathway and transhydrogenase over-expressing strain. Our results show how engineering cofactor dependence can overcome a critical obstacle to next-generation biofuel commercialization.
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Affiliation(s)
- Sabine Bastian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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37
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Forgan RS, Sauvage JP, Stoddart JF. Chemical Topology: Complex Molecular Knots, Links, and Entanglements. Chem Rev 2011; 111:5434-64. [DOI: 10.1021/cr200034u] [Citation(s) in RCA: 650] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ross S. Forgan
- Center for the Chemistry of Integrated Systems and the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Jean-Pierre Sauvage
- Center for the Chemistry of Integrated Systems and the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - J. Fraser Stoddart
- Center for the Chemistry of Integrated Systems and the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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Virnau P, Mallam A, Jackson S. Structures and folding pathways of topologically knotted proteins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:033101. [PMID: 21406854 DOI: 10.1088/0953-8984/23/3/033101] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In the last decade, a new class of proteins has emerged that contain a topological knot in their backbone. Although these structures are rare, they nevertheless challenge our understanding of protein folding. In this review, we provide a short overview of topologically knotted proteins with an emphasis on newly discovered structures. We discuss the current knowledge in the field, including recent developments in both experimental and computational studies that have shed light on how these intricate structures fold.
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Affiliation(s)
- Peter Virnau
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 7, 55128 Mainz, Germany.
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39
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Jacobsen JA, Fullagar JL, Miller MT, Cohen SM. Identifying chelators for metalloprotein inhibitors using a fragment-based approach. J Med Chem 2010; 54:591-602. [PMID: 21189019 DOI: 10.1021/jm101266s] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fragment-based lead design (FBLD) has been used to identify new metal-binding groups for metalloenzyme inhibitors. When screened at 1 mM, a chelator fragment library (CFL-1.1) of 96 compounds produced hit rates ranging from 29% to 43% for five matrix metalloproteases (MMPs), 24% for anthrax lethal factor (LF), 49% for 5-lipoxygenase (5-LO), and 60% for tyrosinase (TY). The ligand efficiencies (LE) of the fragment hits are excellent, in the range of 0.4-0.8 kcal/mol. The MMP enzymes all generally elicit the same chelators as hits from CFL-1.1; however, the chelator fragments that inhibit structurally unrelated metalloenzymes (LF, 5-LO, TY) vary considerably. To develop more advanced hits, one hit from CFL-1.1, 8-hydroxyquinoline, was elaborated at four different positions around the ring system to generate new fragments. 8-Hydroxyquinoline fragments substituted at either the 5- or 7-positions gave potent hits against MMP-2, with IC(50) values in the low micromolar range. The 8-hydroxyquinoline represents a promising new chelator scaffold for the development of MMP inhibitors that was discovered by use of a metalloprotein-focused chelator fragment library.
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Affiliation(s)
- Jennifer A Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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40
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Potestio R, Micheletti C, Orland H. Knotted vs. unknotted proteins: evidence of knot-promoting loops. PLoS Comput Biol 2010; 6:e1000864. [PMID: 20686683 PMCID: PMC2912335 DOI: 10.1371/journal.pcbi.1000864] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 06/22/2010] [Indexed: 11/29/2022] Open
Abstract
Knotted proteins, because of their ability to fold reversibly in the same topologically entangled conformation, are the object of an increasing number of experimental and theoretical studies. The aim of the present investigation is to assess, on the basis of presently available structural data, the extent to which knotted proteins are isolated instances in sequence or structure space, and to use comparative schemes to understand whether specific protein segments can be associated to the occurrence of a knot in the native state. A significant sequence homology is found among a sizeable group of knotted and unknotted proteins. In this family, knotted members occupy a primary sub-branch of the phylogenetic tree and differ from unknotted ones only by additional loop segments. These “knot-promoting” loops, whose virtual bridging eliminates the knot, are found in various types of knotted proteins. Valuable insight into how knots form, or are encoded, in proteins could be obtained by targeting these regions in future computational studies or excision experiments. Out of the tens of thousands of known protein structures, only a few hundred are knotted. The latter epitomize, better than unknotted proteins, the degree of coordinated motion of the backbone required to fold reversibly in a specific native conformation, which indeed must contain a precise knot in a specific protein region. In the present work we search for salient features associated to protein “knottedness” through a systematic sequence and structure comparison of knotted and unknotted protein chains. A significant sequence relatedness is found within a sizeable group of knotted and unknotted proteins. Their tree of sequence relatedness suggests that the knotted entries all diverged from a specific evolutionary event. The systematic structural comparison further indicates that the knottedness of several different types of proteins is likely ascribable to the presence of short “knot-promoting” loops. These segments, whose bridging eliminates the knot, are natural candidates for future experimental/computational studies aimed at clarifying whether the global knotted state of a protein is influenced by specific regions of the primary sequence.
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Affiliation(s)
- Raffaello Potestio
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Cristian Micheletti
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
- DEMOCRITOS CNR-IOM, Trieste, Italy
- Italian Institute of Technology (SISSA unit), Trieste, Italy
- * E-mail:
| | - Henri Orland
- Institut de Physique Théorique, CEA, Gif-sur-Yvette, France
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41
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Binder S. Branched-Chain Amino Acid Metabolism in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2010; 8:e0137. [PMID: 22303262 PMCID: PMC3244963 DOI: 10.1199/tab.0137] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Valine, leucine and isoleucine form the small group of branched-chain amino acids (BCAAs) classified by their small branched hydrocarbon residues. Unlike animals, plants are able to de novo synthesize these amino acids from pyruvate, 2-oxobutanoate and acetyl-CoA. In plants, biosynthesis follows the typical reaction pathways established for the formation of these amino acids in microorganisms. Val and Ile are synthesized in two parallel pathways using a single set of enzymes. The pathway to Leu branches of from the final intermediate of Val biosynthesis. The formation of this amino acid requires a three-step pathway generating a 2-oxoacid elongated by a methylene group. In Arabidopsis thaliana and other Brassicaceae, a homologous three-step pathway is also involved in Met chain elongation required for the biosynthesis of aliphatic glucosinolates, an important class of specialized metabolites in Brassicaceae. This is a prime example for the evolutionary relationship of pathways from primary and specialized metabolism. Similar to animals, plants also have the ability to degrade BCAAs. The importance of BCAA turnover has long been unclear, but now it seems apparent that the breakdown process might by relevant under certain environmental conditions. In this review, I summarize the current knowledge about BCAA metabolism, its regulation and its particular features in Arabidopsis thaliana.
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Affiliation(s)
- Stefan Binder
- Institute Molecular Botany, Ulm University, Albert-Einstein-Allee 11, 89060 Ulm, Germany Address correspondence to
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42
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Leung EWW, Guddat LW. Conformational changes in a plant ketol-acid reductoisomerase upon Mg(2+) and NADPH binding as revealed by two crystal structures. J Mol Biol 2009; 389:167-82. [PMID: 19362563 DOI: 10.1016/j.jmb.2009.04.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 04/02/2009] [Accepted: 04/04/2009] [Indexed: 11/17/2022]
Abstract
Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) is an enzyme in the branched-chain amino acid biosynthesis pathway where it catalyzes the conversion of 2-acetolactate into (2R)-2,3-dihydroxy-3-isovalerate or the conversion of 2-aceto-2-hydroxybutyrate into (2R,3R)-2,3-dihydroxy-3-methylvalerate. KARI catalyzes two reactions-alkyl migration and reduction-and requires Mg(2+) and NADPH for activity. To date, the only reported structures for a plant KARI are those of the spinach enzyme-Mn(2+)-(phospho)ADP ribose-(2R,3R)-2,3-dihydroxy-3-methylvalerate complex and the spinach KARI-Mg(2)(+)-NADPH-N-hydroxy-N-isopropyloxamate complex, where N-hydroxy-N-isopropyloxamate is a predicted transition-state analog. These studies demonstrated that the enzyme consists of two domains, N-domain and C-domain, with the active site at the interface of these domains. Here, we have determined the structures of the rice KARI-Mg(2+) and rice KARI-Mg(2)(+)-NADPH complexes to 1.55 A and 2.80 A resolutions, respectively. In comparing the structures of all the complexes, several differences are observed. Firstly, the N-domain is rotated up to 15 degrees relative to the C-domain, expanding the active site by up to 4 A. Secondly, an alpha-helix in the C-domain that includes residues V510-T519 and forms part of the active site moves by approximately 3.9 A upon binding of NADPH. Thirdly, the 15 C-terminal amino acid residues in the rice KARI-Mg(2+) complex are disordered. In the rice KARI-Mg(2)(+)-NADPH complex and the spinach KARI structures, many of the 15 residues bind to NADPH and the N-domain and cover the active site. Fourthly, the location of the metal ions within the active site can vary by up to 2.7 A. The new structures allow us to propose that an induced-fit mechanism operates to (i) allow substrate to enter the active site, (ii) close over the active site during catalysis, and (iii) open the active site to facilitate product release.
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43
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Dzubiella J. Sequence-specific size, structure, and stability of tight protein knots. Biophys J 2009; 96:831-9. [PMID: 19186124 PMCID: PMC2716640 DOI: 10.1016/j.bpj.2008.10.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 10/20/2008] [Indexed: 11/19/2022] Open
Abstract
Approximately 1% of known protein structures display knotted configurations in their native fold, but the function of these configurations is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Protein knot manipulation, e.g., knot tightening and localization, has become possible in single-molecule experiments. Here, we investigate tight peptide knot (TPK) characteristics in detail by pulling selected 3(1) and 4(1)-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3(1)- and 4(1)-TPK lengths are typically Deltal approximately 47+/- 4 A and 69 +/- 4 A, respectively, for a wide range of tensions (0.1 nN less, similarF less, similar 1.5 nN). The 4(1)-knot length is in agreement with recent atomic force microscopy pulling experiments. Calculated TPK radii of gyration point to a pore diameter of approximately 20 A, below which a translocated knotted protein might get stuck. TPK characteristics, however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water trapping capability of hydrophobic TPKs. Water capture and release is found to be controllable by the tightening force in a few cases. These mechanisms result in a sequence-specific "locking" and metastability of TPKs, which might lead to a blocking of knotted peptide transport at designated sequence positions. We observe that macroscopic tight 4(1)-knot structures are reproduced microscopically ("figure of eight" versus the "pretzel") and can be tuned by sequence, in contrast to mathematical predictions. Our findings may explain a function of knots in native proteins, challenge previous studies on macromolecular knots, and prove useful in bio- and nanotechnology.
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Wang BL, Li YH, Wang JG, Ma Y, Li ZM. Molecular design, synthesis and biological activities of amidines as new ketol-acid reductoisomerase inhibitors. CHINESE CHEM LETT 2008. [DOI: 10.1016/j.cclet.2008.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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He FQ, Liu XH, Wang BL, Li ZM. Synthesis and biological activities of novel bis-heterocyclic pyrrodiazole derivatives. HETEROATOM CHEMISTRY 2008. [DOI: 10.1002/hc.20369] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Yeates TO, Norcross TS, King NP. Knotted and topologically complex proteins as models for studying folding and stability. Curr Opin Chem Biol 2007; 11:595-603. [PMID: 17967433 DOI: 10.1016/j.cbpa.2007.10.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 10/01/2007] [Indexed: 10/22/2022]
Abstract
Among proteins of known three-dimensional structure, only a few possess complex topological features such as knotted or interlinked (catenated) protein backbones. Such unusual proteins offer potentially unique insights into folding pathways and stabilization mechanisms. They also present special challenges for both theorists and computational scientists interested in understanding and predicting protein-folding behavior. Here, we review complex topological features in proteins with a focus on recent progress on the identification and characterization of knotted and interlinked protein systems. Also, an approach is described for designing an expanded set of knotted proteins.
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Affiliation(s)
- Todd O Yeates
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA 90095-1569, USA.
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King NP, Yeates EO, Yeates TO. Identification of rare slipknots in proteins and their implications for stability and folding. J Mol Biol 2007; 373:153-66. [PMID: 17764691 DOI: 10.1016/j.jmb.2007.07.042] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/17/2007] [Accepted: 07/19/2007] [Indexed: 11/27/2022]
Abstract
Among the thousands of known three-dimensional protein folds, only a few have been found whose backbones are in knotted configurations. The rarity of knotted proteins has important implications for how natural proteins reach their natively folded states. Proteins with such unusual features offer unique opportunities for studying the relationships between structure, folding, and stability. Here we report the identification of a unique slipknot feature in the fold of a well-known thermostable protein, alkaline phosphatase. A slipknot is created when a knot is formed by part of a protein chain, after which the backbone doubles back so that the entire structure becomes unknotted in a mathematical sense. Slipknots are therefore not detected by computational tests that look for knots in complete protein structures. A computational survey looking specifically for slipknots in the Protein Data Bank reveals a few other instances in addition to alkaline phosphatase. Unexpected similarities are noted among some of the proteins identified. In addition, two transmembrane proteins are found to contain slipknots. Finally, mutagenesis experiments on alkaline phosphatase are used to probe the contribution the slipknot feature makes to thermal stability. The trends and conserved features observed in these proteins provide new insights into mechanisms of protein folding and stability.
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Affiliation(s)
- Neil P King
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095-1569, USA
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Liu XH, Chen PQ, Wang BL, Li YH, Wang SH, Li ZM. Synthesis, bioactivity, theoretical and molecular docking study of 1-cyano-N-substituted-cyclopropanecarboxamide as ketol-acid reductoisomerase inhibitor. Bioorg Med Chem Lett 2007; 17:3784-8. [PMID: 17512731 DOI: 10.1016/j.bmcl.2007.04.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 03/15/2007] [Accepted: 04/02/2007] [Indexed: 11/24/2022]
Abstract
Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) catalyzes the second common step in branched-chain amino acid biosynthesis. The catalyzed process consists of two stages, the first of which is an alkyl migration from one carbon atom to its neighbouring atom. The likely transition state is a cyclopropane derivative, thus a series of new cyclopropane derivatives, such as 1-cyano-N-substituted-cyclopropanecarboxamide, were designed and synthesized. Their structures were verified by (1)H NMR, FTIR spectrum, MS and elemental analysis. The K(i) values of active compounds 2, 4b against rice KARI were 95.30+/-13.71, 207.9+/-21.99 microM, respectively. The X-ray crystal structure of compound 4a was also determined. Auto-Dock was used to predict the binding mode of 4a. This was done by analyzing the interaction of the compounds 4a with the active sites of spinach KARI. This result was in accord with the result analyzed by the frontier molecular orbital theory.
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Affiliation(s)
- Xing-Hai Liu
- The Research Institute of Elemento-Organic Chemistry, The State-Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, Nankai University, Tianjin 300071, China
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Taylor WR. Protein knots and fold complexity: Some new twists. Comput Biol Chem 2007; 31:151-62. [PMID: 17500039 DOI: 10.1016/j.compbiolchem.2007.03.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 03/17/2007] [Indexed: 10/23/2022]
Abstract
The current knowledge on topological knots in protein structure is reviewed, considering in turn, knots with three, four and five strand crossings. The latter is the most recent to be identified and has two distinct topological forms. The knot observed in the protein structure is the form that requires the least number of strand crossings to become un-knotted. The position of the chain termini must also correspond to a position that allows (un) knotting in one move. This is postulated as a general property of protein knots and other more complex knots with this property are proposed as the next most likely knots that might be found in a protein. It is also noted that the "Jelly-roll" fold found in some all-beta proteins would provide likely candidates. Alternative measures of knottedness and entanglement are reviewed, including the occurrence of slip-knots. These measures are related to the complexity of the protein fold and may provide useful filters for selecting predicted model structures.
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Affiliation(s)
- William R Taylor
- Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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Ciulli A, Lobley CMC, Tuck KL, Smith AG, Blundell TL, Abell C. pH-tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2007; 63:171-8. [PMID: 17242510 PMCID: PMC2483484 DOI: 10.1107/s0907444906044465] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Accepted: 10/25/2006] [Indexed: 11/12/2022]
Abstract
The crystal structure of Escherichia coli ketopantoate reductase in complex with 2'-monophosphoadenosine 5'-diphosphoribose, a fragment of NADP+ that lacks the nicotinamide ring, is reported. The ligand is bound at the enzyme active site in the opposite orientation to that observed for NADP+, with the adenine ring occupying the lipophilic nicotinamide pocket. Isothermal titration calorimetry with R31A and N98A mutants of the enzyme is used to show that the unusual ;reversed binding mode' observed in the crystal is triggered by changes in the protonation of binding groups at low pH. This research has important implications for fragment-based approaches to drug design, namely that the crystallization conditions and the chemical modification of ligands can have unexpected effects on the binding modes.
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Affiliation(s)
- Alessio Ciulli
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, England
| | - Carina M. C. Lobley
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
| | - Kellie L. Tuck
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, England
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, England
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
| | - Chris Abell
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, England
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